data<-read.table("graph_dosage.txt",sep=" ")
dim(data)
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10])
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,100,0.01),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy")
hist(data[,10],breaks=seq(0,700,0.01),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10])
dev.off()
max(data[,10])
min(data[,10])
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,0.5),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,10),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,1),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy (Dosage)")
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),xlab="Absolute mean",ylab ="counts",main="Beagle imputation accuracy (Dosage)")
dev.off()
pdf("beagle_concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
dev.off()
pdf("impute_concord_dosage_hist.pdf")
data[1,]
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,100),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,100),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,100),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,100),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Absolute Dosage difference mean",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Mean of Absolute Dosage difference ",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Mean of absolute dosage difference",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("Concord_dosage_hist.pdf")
hist(data[,10],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Mean of absolute dosage difference ",ylab ="Number of Samples",main="Beagle imputation accuracy (Dosage)")
hist(data[,8],breaks=seq(0,700,2),xlim=c(0,700),ylim=c(1,75),xlab="Mean of absolute dosage difference",ylab ="Number of Samples",main="Impute imputation accuracy (Dosage)")
dev.off()
pdf("scatter_plot_dosage_maf.pdf")
data[1,]
plot(data[,5],data[,10],xlim=c(0,1),main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,8],xlim=c(0,1),main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
dev.off()
pdf("scatter_plot_dosage_maf.pdf")
plot(data[,5],data[,10],xlim=c(0,0.5),ylim=c(0,700)main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,10],xlim=c(0,0.5),ylim=c(0,700),main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,8],xlim=c(0,0.5),ylim=c(0,700),main="Impute Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
dev.off()
pdf("scatter_plot_dosage.pdf")
plot(data[,10],data[,8],xlim=c(0,700),ylim=c(0,700),main="Beagle vs Impute",ylab="Impute Dosage Difference",xlab="Beagle Dosage Difference",pch="*")
abline(lm(data[,8]~data[,10]), col="red")
dev.off()
savehistory("Rscript_dosage_comapare.R")
